How to search sequences in bulk？

[1185307269]

Dear all:
I have a question: How can I do a bulk search sequences in the web version?

Or can I download it through an API?

[tomsercu]

Unfortunately we don't support bulk sequence search, you should use mmseqs directly. We'll upload a fasta file and pre-computed mmseqs db.

[1185307269]

Thank you very much for your reply!
Where can I download the fasta file and the pre-computed mmseqs db?

[ebetica]

I uploaded the high quality fasta here:

s3://dl.fbaipublicfiles.com/esmatlas/v0/highquality_clust30/highquality_clust30.fasta

And mgnify90 here:

s3://dl.fbaipublicfiles.com/esmatlas/v0/full/mgnify90.fasta

[1185307269]

Thank you very much for your reply！！！！！But I have one more stupid question to ask: what is the difference between these two databases? If I have some sequences to search, which database should I take for searching?

[ebetica]

The high quality is a subset of mgnify90 which is redundancy reduced and well predicted by ESMFold (pTM & pLDDT > 0.7)

[tomsercu]

We now provide https://dl.fbaipublicfiles.com/esmatlas/v0/full/atlas.fasta with 617051007 records precisely matching stats.parquet.

See #366 for more context